Regime shifts are major reorganization of ecological processes, creating new sets of mechanisms that drive the new ecological regime. Such rearrangements can affect how and how much the system responds to pressures other than those that created the shift (interactive carryover). Lake Geneva still exhibits high levels of productivity despite reductions in phosphorus to its reference baseline; the continued high productivity is likely due to the synergistic effects of climate change. We tested whether the contemporary Lake Geneva plankton community response to air temperature, one symptom of climate change, differed from the responses to past changes in air temperature. We used paleoecology to quantify the changes in plankton communities, as a proxy of general ecological changes, over the past 1500 years. Our results show that from 563 AD (beginning of the record) to the twentieth century, the cladoceran assemblage remained stable, despite climate variability of 3 °C in air temperature. The plankton community of Lake Geneva appeared to shift for the first time in the 1500 year record in 1946, and dynamic linear models suggested that 1958–1961 was a critical transition period when the ecosystem changed state. Littoral species were lost, and the assemblage became dominated by pelagic species. The shift took place around the beginning of the current long-term monitoring program, when local perturbations (eutrophication) were escalating. Our results suggest that eutrophication acted as a switch towards a lake more vulnerable to climate change.